Algorithms on strings, trees, and sequences: computer science and computational biology
Algorithms on strings, trees, and sequences: computer science and computational biology
Computing the local consensus of trees
Proceedings of the sixth annual ACM-SIAM symposium on Discrete algorithms
Proceedings of the seventh annual ACM-SIAM symposium on Discrete algorithms
Recovering branches on the tree of life: an approximation algorithm
Proceedings of the tenth annual ACM-SIAM symposium on Discrete algorithms
Computing the quartet distance between evolutionary trees
SODA '00 Proceedings of the eleventh annual ACM-SIAM symposium on Discrete algorithms
A supertree method for rooted trees
Discrete Applied Mathematics
Incomplete Directed Perfect Phylogeny
COM '00 Proceedings of the 11th Annual Symposium on Combinatorial Pattern Matching
Using Max Cut to Enhance Rooted Trees Consistency
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
An improved fixed-parameter algorithm for minimum-flip consensus trees
IWPEC'08 Proceedings of the 3rd international conference on Parameterized and exact computation
Exact ILP solutions for phylogenetic minimum flip problems
Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology
Using semi-definite programming to enhance supertree resolvability
WABI'05 Proceedings of the 5th International conference on Algorithms in Bioinformatics
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The input to a supertree problem is a collection of phylogenetic trees that intersect pairwise in their leaf sets; the goal is to construct a single tree that retains as much as possible of the information in the input. This task is complicated by inconsistencies due to errors. We consider the case where the source trees are rooted and are represented by the clusters they exhibit. The problem is to find the minimum number of flips needed to resolve all inconsistencies, where each flip moves a taxon into or out of a cluster. We prove that the minimum flip problem is NP-complete, but show that it is fixed-parameter tractable and give an approximation algorithm for a special case.